hmm..upgrading over existing 98 installs...even a simple upgrade to SE, is bound to cause problems. that's why i always do a fresh install after formatting when i upgrade OS's
do you have the 98se upgrade cd? or the full retail 98SE cd? if you have the full retail, i would highly suggest a re-install. there are usually just too many variables to pinpoint why you would be crashing, but you can be 99% guaranteed that re-installing would fix the problem.